In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage
dc.contributor.author | Huang, Po Jung Jimmy | |
dc.contributor.author | Vazin, Mahsa | |
dc.contributor.author | Liu, Juewen | |
dc.date.accessioned | 2017-04-28T16:11:57Z | |
dc.date.available | 2017-04-28T16:11:57Z | |
dc.date.issued | 2016-05-03 | |
dc.description | This document is the Accepted Manuscript version of a Published Work that appeared in final form in Biochemistry, © 2016 American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Huang, P. J. J., Vazin, M., & Liu, J. (2016). In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage. Biochemistry, 55(17), 2518–2525. https://doi.org/10.1021/acs.biochem.6b00132 | en |
dc.description.abstract | Trivalent lanthanide ions (Ln(3+)) were recently employed to select RNA-cleaving DNAzymes, and three new DNAzymes have been reported so far. In this work, dysprosium (Dy3+) was used with a library containing 50 random nucleotides. After six rounds of in vitro selection, a new DNAzyme named Dy10a was obtained and characterized. Dy10a has a bulged hairpin structure cleaving a RNA/DNA chimeric substrate. Dy10a is highly active in the presence of the five Ln(3+) ions in the middle of the lanthanide series (Sm3+, Eu3+, Gd3+, Tb3+, and Dy3+), while its activity descends on the two sides. The cleavage rate reaches 0.6 min(-1) at pH 6 with just 200 nM Sm3+, which is the fastest among all known Ln(3+)-dependent enzymes. Dy10a binds two Ln(3+) ions cooperatively. When a phosphorothioate (PS) modification is introduced at the cleavage junction, the activity decreases by >2500-fold for both the R-p and S-p diastereomers, and thiophilic Cd2+ cannot rescue the activity. The pH-rate profile has a slope of 0.37 between pH 4.2 and 5.2, and the slope was even lower at higher pH. On the basis of these data, a model of metal binding is proposed. Finally, a catalytic beacon sensor that can detect Ho3+ down to 1.7 nM is constructed. | en |
dc.description.sponsorship | Natural Sciences and Engineering Research Council (NSERC) of Canada [386326, STPGP 447472-13] | en |
dc.identifier.uri | http://dx.doi.org/10.1021/acs.biochem.6b00132 | |
dc.identifier.uri | http://hdl.handle.net/10012/11789 | |
dc.language.iso | en | en |
dc.publisher | American Chemical Society | en |
dc.subject | Delta Virus Ribozyme | en |
dc.subject | Metal-Ion | en |
dc.subject | Dependent DNAzyme | en |
dc.subject | Cleaving Deoxyribozyme | en |
dc.subject | Catalytic DNA | en |
dc.subject | Phosphorothioate | en |
dc.subject | Site | en |
dc.subject | Sensor | en |
dc.subject | Lead | en |
dc.subject | Hydrolysis | en |
dc.title | In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage | en |
dc.type | Article | en |
dcterms.bibliographicCitation | Huang, P. J. J., Vazin, M., & Liu, J. (2016). In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage. Biochemistry, 55(17), 2518–2525. https://doi.org/10.1021/acs.biochem.6b00132 | en |
uws.contributor.affiliation1 | Faculty of Science | en |
uws.contributor.affiliation2 | Chemistry | en |
uws.contributor.affiliation3 | Waterloo Institute for Nanotechnology (WIN) | en |
uws.peerReviewStatus | Reviewed | en |
uws.scholarLevel | Faculty | en |
uws.typeOfResource | Text | en |
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